Misfolded membrane proteins are specifically recognized by the transmembrane domain of the Hrd1p ubiquitin ligase.

Quality control pathways such as ER-associated degradation (ERAD) employ a small number of factors to specifically recognize a wide variety of protein substrates. Delineating the mechanisms of substrate selection is a principle goal in studying quality control. The Hrd1p ubiquitin ligase mediates ERAD of numerous misfolded proteins including soluble, lumenal ERAD-L and membrane-anchored ERAD-M substrates. We tested if the Hrd1p multispanning membrane domain was involved in ERAD-M specificity. In this work, we have identified site-directed membrane domain mutants of Hrd1p impaired only for ERAD-M and normal for ERAD-L. Furthermore, other Hrd1p variants were specifically deficient for degradation of individual ERAD-M substrates. Thus, the Hrd1p transmembrane region bears determinants of high specificity in the ERAD-M pathway. From in vitro and interaction studies, we suggest a model in which the Hrd1p membrane domain employs intramembrane residues to evaluate substrate misfolding, leading to selective ubiquitination of appropriate ERAD-M clients.

Mechanisms of cardiac and renal dysfunction in patients dying of sepsis.

RATIONALE: The mechanistic basis for cardiac and renal dysfunction in sepsis is unknown. In particular, the degree and type of cell death is undefined. OBJECTIVES: To evaluate the degree of sepsis-induced cardiomyocyte and renal tubular cell injury and death. METHODS: Light and electron microscopy and immunohistochemical staining for markers of cellular injury and stress, including connexin-43 and kidney-injury-molecule-1 (Kim-1), were used in this study. MEASUREMENTS AND MAIN RESULTS: Rapid postmortem cardiac and renal harvest was performed in 44 septic patients. Control hearts were obtained from 12 transplant and 13 brain-dead patients. Control kidneys were obtained from 20 trauma patients and eight patients with cancer. Immunohistochemistry demonstrated low levels of apoptotic cardiomyocytes (<1-2 cells per thousand) in septic and control subjects and revealed redistribution of connexin-43 to lateral membranes in sepsis (P < 0.020). Electron microscopy showed hydropic mitochondria only in septic specimens, whereas mitochondrial membrane injury and autophagolysosomes were present equally in control and septic specimens. Control kidneys appeared relatively normal by light microscopy; 3 of 20 specimens showed focal injury in approximately 1% of renal cortical tubules. Conversely, focal acute tubular injury was present in 78% of septic kidneys, occurring in 10.3 ± 9.5% and 32.3 ± 17.8% of corticomedullary-junction tubules by conventional light microscopy and Kim-1 immunostains, respectively (P < 0.01). Electron microscopy revealed increased tubular injury in sepsis, including hydropic mitochondria and increased autophagosomes. CONCLUSIONS: Cell death is rare in sepsis-induced cardiac dysfunction, but cardiomyocyte injury occurs. Renal tubular injury is common in sepsis but presents focally; most renal tubular cells appear normal. The degree of cell injury and death does not account for severity of sepsis-induced organ dysfunction.

How syllabi relate to outcomes in higher education: A study of syllabi learner-centeredness and grade inequities in STEM.

Fostering equity in undergraduate science, technology, engineering, and mathematics (STEM) programs can be accomplished by incorporating learner-centered pedagogies, resulting in the closing of opportunity gaps (defined here as the difference in grades earned by minoritized and non-minoritized students). We assessed STEM courses that exhibit small and large opportunity gaps at a minority-serving, research-intensive university, and evaluated the degree to which their syllabi are learner-centered, according to a previously validated rubric. We specifically chose syllabi as they are often the first interaction students have with a course, establish expectations for course policies and practices, and serve as a proxy for the course environment. We found STEM courses with more learner-centered syllabi had smaller opportunity gaps. The syllabus rubric factor that most correlated with smaller gaps was Power and Control, which reflects Student's Role, Outside Resources, and Syllabus Focus. This work highlights the importance of course syllabi as a tool for instructors to create more inclusive classroom environments.

Instructional Influencers: Teaching Professors as Potential Departmental Change Agents in Diversity, Equity, and Inclusion.

At many research-intensive universities in North America, there is a disproportionate loss of minoritized undergraduate students from Science, Technology, Engineering, and Mathematics (STEM) majors. Efforts to confront this diversity, equity, and inclusion (DEI) challenge, such as faculty adoption of evidenced-based instructional approaches that promote student success, have been slow. Instructional and pedagogical change efforts at the academic department level have been demonstrated to be effective at enacting reform. One potential strategy is to embed change agent individuals within STEM departments that can drive change efforts. This study seeks to assess whether tenure-track, teaching-focused faculty housed in STEM departments are perceived as influential on the instructional and pedagogical domains of their colleagues. To answer this, individuals across five STEM departments at large, research-intensive campuses identified faculty who were influential upon six domains of their instruction and pedagogy. Social network analysis of individuals in these departments revealed heterogeneity across the instructional domains. Some, like the teaching strategies network, are highly connected and involve the majority of the department; while others, like the DEI influence network, comprise a significantly smaller population of faculty. Importantly, we demonstrate that tenure-track, teaching-focused faculty are influential across all domains of instruction, but are disproportionately so in the sparsely populated DEI influence networks.

A Multi-institutional Cluster Analysis to Identify Groups of Courses with Exemplary Opportunity Gaps for Undergraduate Students in the Biological Sciences.

Examining institutional data from seven cohorts of students intending to major in biology across five research-intensive institutions, this work analyzes opportunity gaps-defined as the difference between the grade received by students from the dominant and nondominant sociodemographic groups in institutions of higher education-at the course-section level across mathematics, physics, biology, and chemistry disciplines. From this analysis, we find that the majority of course sections have large opportunity gaps between female and male students, students who are Black, Latino/a/e/x, or indigenous to the United States and its territories and students who are White or Asian, first-generation and non-first-generation students, and low-income and non-low-income students. This work provides a framework to analyze equity across institutions using robust methodology, including: using multiple approaches to measure grades, quantile regression rankscores which adjust for previous academic performance, and cluster analysis. Recommendations are provided for institutions to identify faculty who have equitable course sections, automate equity analyses, and compare results to other institutions to make a change toward more equitable outcomes.

Identifying systemic inequity in higher education and opportunities for improvement.

It is well established that there is a national problem surrounding the equitable participation in and completion of science, technology, engineering, and mathematics (STEM) higher education programs. Persons excluded because of their ethnicity or race (PEERs) experience lower course performance, major retention, sense of belonging, and degree completion. It is unclear though how pervasive these issues are across an institution, from the individual instructor, course, and discipline perspectives. Examining over six years of institutional data from a large-enrollment, research-intensive, minority-serving university, we present an analysis of racial opportunity gaps between PEERs and non-PEERs to identify the consistency of these issues. From this analysis, we find that there is considerable variability as to whether a given course section taught by a single instructor does or does not exhibit opportunity gaps, although encouragingly we did identify exemplar instructors, course-instructor pairs, courses, and departments that consistently had no significant gaps observed. We also identified significant variation across course-instructor pairs within a department, and found that certain STEM disciplines were much more likely to have courses that exhibited opportunity gaps relative to others. Across nearly all disciplines though, it is clear that these gaps are more pervasive in the lower division curriculum. This work highlights a means to identify the extent of inequity in STEM success across a university by leveraging institutional data. These findings also lay the groundwork for future studies that will enable the intentional design of STEM education reform by leveraging beneficial practices used by instructors and departments assigning equitable grades.

Moving the Needle: Evidence of an Effective Study Strategy Intervention in a Community College Biology Course.

Many science, technology, engineering, and math (STEM) community college students do not complete their degree, and these students are more likely to be women or in historically excluded racial or ethnic groups. In introductory courses, low grades can trigger this exodus. Implementation of high-impact study strategies could lead to increased academic performance and retention. The examination of study strategies rarely occurs at the community college level, even though community colleges educate approximately half of all STEM students in the United States who earn a bachelor's degree. To fill this research gap, we studied students in two biology courses at a Hispanic-serving community college. Students were asked their most commonly used study strategies at the start and end of the semester. They were given a presentation on study skills toward the beginning of the semester and asked to self-assess their study strategies for each exam. We observed a significantly higher course grade for students who reported spacing their studying and creating drawings when controlling for demographic factors, and usage of these strategies increased by the end of the semester. We conclude that high-impact study strategies can be taught to students in community college biology courses and result in higher course performance.

Bootleg Biology: a Semester-Long CURE Using Wild Yeast to Brew Beer.

Laboratory exercises for undergraduates that involve authentic discovery and research have been shown to increase student learning and engagement. To bring these advantages into the microbiology curriculum, we developed a semester-long course-based undergraduate research experience for a laboratory based on brewing beer with wild yeast. This set of lab exercises uses many of the same protocols found in traditional microbiology lab curricula-isolating and maintaining pure cultures, staining and microscopy, use of aseptic technique, PCR, gel electrophoresis, and media preparation-and integrates them into a novel and exciting project that enables students to be active participants in the scientific method. Students are assessed on their ability to brew beer successfully and to stain and visualize microorganisms; they are also assessed for knowledge gains in the traditional portion of the course, their ability to use their brewing knowledge in other settings, and their attitudes about science. After completing the course, students showed gains in general microbiology knowledge and their engagement with science.

Moving towards More Diverse and Welcoming Conference Spaces: Data-Driven Perspectives from Biology Education Research Scholars.

Academic conferences are integral to the dissemination of novel research findings and discussion of pioneering ideas across all postsecondary disciplines. For some participants, these environments are spaces to develop new collaborations, research projects, and social bonds; however, for others, conferences can be a place of marginalization and outright hostility. To assess how diverse individuals experience conference spaces, we interpreted results from a conference climate survey filled out by 198 of 482 registrants of the Society for the Advancement of Biology Education Research (SABER) West 2021 conference. Analysis of the survey data was conducted by six biology education researchers, who in addition to raising conference participant voices, provide insights, and next steps whose implementation can promote greater participant equity, representation, and engagement in future science, technology, engineering, and math (STEM) education conferences specifically and potentially all academic conference spaces more broadly.

Predicting implementation of active learning by tenure-track teaching faculty using robust cluster analysis.

Background: The University of California system has a novel tenure-track education-focused faculty position called Lecturer with Security of Employment (working titles: Teaching Professor or Professor of Teaching). We focus on the potential difference in implementation of active-learning strategies by faculty type, including tenure-track education-focused faculty, tenure-track research-focused faculty, and non-tenure-track lecturers. In addition, we consider other instructor characteristics (faculty rank, years of teaching, and gender) and classroom characteristics (campus, discipline, and class size). We use a robust clustering algorithm to determine the number of clusters, identify instructors using active learning, and to understand the instructor and classroom characteristics in relation to the adoption of active-learning strategies. Results: We observed 125 science, technology, engineering, and mathematics (STEM) undergraduate courses at three University of California campuses using the Classroom Observation Protocol for Undergraduate STEM to examine active-learning strategies implemented in the classroom. Tenure-track education-focused faculty are more likely to teach with active-learning strategies compared to tenure-track research-focused faculty. Instructor and classroom characteristics that are also related to active learning include campus, discipline, and class size. The campus with initiatives and programs to support undergraduate STEM education is more likely to have instructors who adopt active-learning strategies. There is no difference in instructors in the Biological Sciences, Engineering, or Information and Computer Sciences disciplines who teach actively. However, instructors in the Physical Sciences are less likely to teach actively. Smaller class sizes also tend to have instructors who teach more actively. Conclusions: The novel tenure-track education-focused faculty position within the University of California system represents a formal structure that results in higher adoption of active-learning strategies in undergraduate STEM education. Campus context and evolving expectations of the position (faculty rank) contribute to the symbols related to learning and teaching that correlate with differential implementation of active learning. Supplementary Information: The online version contains supplementary material available at 10.1186/s40594-022-00365-9.

Comparison of Cluster Analysis Methodologies for Characterization of Classroom Observation Protocol for Undergraduate STEM (COPUS) Data.

The Classroom Observation Protocol for Undergraduate STEM (COPUS) provides descriptive feedback to instructors by capturing student and instructor behaviors occurring in the classroom. Due to the increasing prevalence of COPUS data collection, it is important to recognize how researchers determine whether groups of courses or instructors have unique classroom characteristics. One approach uses cluster analysis, highlighted by a recently developed tool, the COPUS Analyzer, that enables the characterization of COPUS data into one of seven clusters representing three groups of instructional styles (didactic, interactive, and student centered). Here, we examine a novel 250 course data set and present evidence that a predictive cluster analysis tool may not be appropriate for analyzing COPUS data. We perform a de novo cluster analysis and compare results with the COPUS Analyzer output and identify several contrasting outcomes regarding course characterizations. Additionally, we present two ensemble clustering algorithms: 1) k-means and 2) partitioning around medoids. Both ensemble algorithms categorize our classroom observation data into one of two clusters: traditional lecture or active learning. Finally, we discuss implications of these findings for education research studies that leverage COPUS data.

Characterizing Biology Education Research: Perspectives from Practitioners and Scholars in the Field.

Biology education research (BER) is a recently emerging field mainly focused on the learning and teaching of biology in postsecondary education. As BER continues to grow, exploring what goals, questions, and scholarship the field encompasses will provide an opportunity for the community to reflect on what new lines of inquiry could be pursued in the future. There have been top-down approaches at characterizing BER, such as aims and scope provided by professional societies or peer-reviewed journals, and literature analyses with evidence for current and historical research trends. However, there have not been previous attempts with a bottom-up approach at characterizing BER by directly surveying practitioners and scholars in the field. Here, we share survey results that asked participants at the Society for the Advancement of Biology Education Research (SABER) annual meeting what they perceive as current scholarship in BER as well as what areas of inquiry in the field that they would like to see pursued in the future. These survey responses provide us with information directly from BER practitioners and scholars, and we invite colleagues to reflect on how we can collectively and collaboratively continue to promote BER as a field.

Instructor facilitation mediates students' negative perceptions of active learning instruction.

Studies have demonstrated students' resistance to active learning, despite evidence illustrating that their learning is improved relative to students in lectures. Specifically, while active learning and group work are effective at engaging students in their learning process, studies report that students' perceptions of active learning approaches are not always positive. What remains underexplored is whether students' perceptions of active learning improve with effective instructor facilitation and whether there exists differential perceptions between racially minoritized students and represented students. Here, we estimate students' perceptions of effective instructor facilitation as the mediator in the relationship between active learning and perceptions of learning and perceived utility for class activities (task value). Then, we examine differences by racial identification. We collected classroom observation data to empirically categorize courses as active learning or lecture-based and surveyed 4,257 college students across 25 STEM classrooms at a research-intensive university. We first examined the relationship between active learning on student perceptions and found a negative relationship between active learning and perceptions of learning and task value for both racially minoritized students and represented students. Next, we assessed whether students' perceptions of instructor effectiveness in facilitating group activities mediate these negative relationships. We found that, on average, students of all races were more likely to positively perceive instructor facilitation in active learning classes relative to lectures. In turn, the positive perceptions of instructor facilitation partially suppressed the negative relationship between active learning and perceptions of learning and task value. These results demonstrate that effective instructor facilitation can influence both students' self-assessment of learning and perceived utility of the learning activities, and underscores the importance of developing pedagogical competence among college instructors.

Characterizing the University of California's tenure-track teaching position from the faculty and administrator perspectives.

Teaching faculty are a potential mechanism to generate positive change in undergraduate STEM education. One such type of faculty is the Lecturer with Potential Security of Employment (L(P)SOE), a tenure-track faculty line within the University of California (UC) system. As a foundation for future studies, we sought to characterize individuals in the L(P)SOE position in terms of their background training, job expectations, and resources available for their success. Data were collected through an online survey completed by over 80% of STEM L(P)SOEs across the UC system, as well as interviews with over 20 deans and chairs in STEM departments at three UC campuses. From this work, we found that the majority of current L(P)SOEs were formally trained within their disciplines and not in an education field; however, they possessed substantial education experience, such as classroom teaching or participation in professional development opportunities. Expectations for time spent on teaching, research, and service are aligned between individuals within varying ranks of the L(P)SOE faculty and between L(P)SOEs and administrators. L(P)SOEs and administrators are also in agreement about what constitutes acceptable professional development activities. Interestingly, we identified differences that may reflect changes in the position over time, including increased start-up funds for more recently hired L(P)SOE faculty and a differing perspective on the role of discipline-based education research and scholarly activities between non-tenured and more senior L(P)SOEs. Overall, these data provide a snapshot of the L(P)SOE position that will aid in future work to identify the potential institutional impact of these individuals.

Testing the test: Are exams measuring understanding?

Grades in undergraduate science, technology, engineering, and mathematics (STEM) courses are distributed under the assumption that high-performing students have a strong understanding of the material. Similarly, the STEM education literature often presents exam performance as equivalent to understanding. Despite these assumptions, we have little knowledge regarding student thinking in relation to exam scores. To investigate this relationship, we asked undergraduate students to complete a series of written and verbal tasks. Twenty-two participants were presented with biology questions and were instructed to write exam-like responses along with their thought process. More than half of the participants then took part in retrospective interviews. We graded the exam-like responses to award a performance score and coded the entirety of participants' writing for their understanding. We found a discrepancy between performance and understanding for over one quarter of our data. Furthermore, interviews allowed for a more complete picture of participant understanding than written responses. These results contribute to calls for re-evaluating our course assessments and for questioning the understanding those assessments value. © 2019 International Union of Biochemistry and Molecular Biology, 47(3):296-302, 2019.

Success with EASE: Who benefits from a STEM learning community?

During the past few decades, there has been a nationwide push to improve performance and persistence outcomes for STEM undergraduates. As part of this effort, recent research has emphasized the need for focus on not only improving the delivery of course content, but also addressing the social-psychological needs of students. One promising intervention type that has been proposed as a multifaceted way to address both cognitive and social-psychological aspects of the learning process is the learning community. Learning communities provide students with opportunities to build a strong support system in college and are generally associated with increased student engagement and integration with campus systems and cultures. In this study, we examine the impact of a learning community intervention for first-year biological sciences majors, the Enhanced Academic Success Experience (EASE) program. Incoming freshmen are assigned to EASE based on their SAT (or ACT equivalent) Math score, a metric demonstrated to be a key predictor of student success in the program. We find that enrollment in EASE is correlated with higher STEM course grades; an increase of 0.25 (on a 0-4 point scale) in cumulative first-year GPA; and gains in non-academic outcomes, such as measures of sense of belonging and academic integration. Further, these outcomes are more pronounced for particular subgroup populations. For example, whereas surveyed male students seemed to benefit academically from participating in a learning community, female students reported a greater sense of belonging in regard to the biological sciences major and reported higher values for behavioral indicators of academic integration. Lastly, we find that the EASE program is positively correlated with students' intention to stay in the biological sciences major. And, among the three race-oriented groups, this impact is most pronounced for under-represented students. In light of these findings, we discuss the potential of discipline-specific learning community programs to improve academic outcomes for students most at risk of leaving STEM majors, such as students underprepared for college level coursework.

Just Figures: A Method to Introduce Students to Data Analysis One Figure at a Time.

Quantitative data analysis skills are basic competencies students in a STEM field should master. In this article, we describe a classroom activity using isolated figures from papers as a simple exercise to practice data analysis skills. We call this approach Just Figures. With this technique, instructors find figures from primary papers that address key concepts related to several of their course learning objectives. These figures are assigned as homework prior to class discussion. In class, instructors teach the lesson and include a 10- to 20-minute discussion of the figures assigned. Frequent and repeated discussion of paper figures during class increased students' confidence in reading and analyzing data. The Just Figures approach also increased student accuracy when interpreting data. After six weeks of Just Figures practice, students scored, on average, three points higher on a 20-point data analysis assessment instrument than they had done before the Just Figures exercises. In addition, a course in which students consistently practiced Just Figures performed just as well on the data analysis assessment instrument and on a class exam dedicated to paper reading compared with courses where students practiced reading three entire papers. The Just Figures method is easy to implement and can effectively improve student data analysis skills in microbiology classrooms.

Prevailing Questions and Methodologies in Biology Education Research: A Longitudinal Analysis of Research in CBE-Life Sciences Education and at the Society for the Advancement of Biology Education Research.

Biology education research (BER) is a growing field, as evidenced by the increasing number of publications in CBE-Life Sciences Education ( LSE) and expanding participation at the Society for the Advancement of Biology Education Research (SABER) annual meetings. To facilitate an introspective and reflective discussion on how research within LSE and at SABER has matured, we conducted a content analysis of LSE research articles ( n = 339, from 2002 to 2015) and SABER abstracts ( n = 652, from 2011 to 2015) to examine three related intraresearch parameters: research questions, study contexts, and methodologies. Qualitative data analysis took a combination of deductive and inductive approaches, followed by statistical analyses to determine the correlations among different parameters. We identified existing research questions, study contexts, and methodologies in LSE articles and SABER abstracts and then compared and contrasted these parameters between the two data sources. LSE articles were most commonly guided by descriptive research questions, whereas SABER abstracts were most commonly guided by causal research questions. Research published in LSE and presented at SABER both prioritize undergraduate classrooms as the study context and quantitative methodologies. In this paper, we examine these research trends longitudinally and discuss implications for the future of BER as a scholarly field.

How do students study in STEM courses? Findings from a light-touch intervention and its relevance for underrepresented students.

With the nationwide emphasis on improving outcomes for STEM undergraduates, it is important that we not only focus on modifying classroom instruction, but also provide students with the tools to maximize their independent learning time. There has been considerable work in laboratory settings examining two beneficial practices for enhancing learning: spacing and self-testing. In the current study, we examine biology students' study practices, particularly in the context of these two behaviors. We specifically investigate whether a light-touch study skills intervention focused on encouraging spacing and self-testing practices impacted their utilization. Based on pre- and post-course surveys, we found that students report utilizing both beneficial and ineffective study practices and confirm that usage of spacing and self-testing correlates with a higher course grade. We also found that students in the section of the course which received the study skills intervention were more likely to report continued use or adoption of spacing and self-testing compared to students in control sections without the intervention. Surprisingly, we found that underrepresented minorities (URMs) under-utilize self-testing, and that our intervention helped to partially ameliorate this gap. Additionally, we found that URMs who reported self-testing earned similar course grades compared to non-URMs who also self-tested, but that there was a much larger drop in performance for URMs who did not self-test relative to non-URMs who also did not self-test. Overall, we would encourage instructors to dedicate class time towards discussing the merits of beneficial study practices, especially for students that have historically underperformed in STEM disciplines.

Understanding Patterns of Socioeconomic and Demographic Factors Along With Health Services Provider Availability for Zika Outbreak in South Florida.

In this study, we analyzed the patterns of socioeconomic and demographic factors along with health services provider availability for the current Zika outbreak in Miami-Dade County, South Florida. We used Center for Consumer Information & Insurance Oversight (CCIIO) Machine-Readable Public Use Files (MR-PUFs) to examine provider availability in combination with socioeconomic and demographic factors that could potentially lead to healthcare disparities between any underserved population of the Wynwood neighborhood and the broader population of Miami-Dade County. MR-PUFs contain public provider-level data from states that are participating in the Federally Facilitated Marketplace. According to CCIIO, an issuer of a Qualified Health Plan that uses a provider network must maintain a network that is sufficient in the number and types of providers, including providers that specialize in mental-health and substance-use disorder services, to assure that all services will be accessible to enrollees without unreasonable delay. (Disaster Med Public Health Preparedness. 2018;12:455-459).